Aitken was appointed manager of Aberdeen in February 1995 after the sacking of Willie Miller.[3][4] At the time, Aberdeen were struggling to avoid relegation, and Aitken made a bright start by winning 2-0 against Rangers in his first game as manager.[4] Aberdeen finished second bottom of the league, but maintained their top league status by defeating Dunfermline Athletic in a two-legged play-off.[4][5]

The following season saw Aitken invest heavily in the transfer market; signing striker Dean Windass for £750,000 and midfielder Paul Bernard for a club record £1 million.[4] Bernard struggled to justify his expensive transfer fee,[6] whilst Windass' time at Pittodrie was hampered by his on-field indiscipline.[7] Nevertheless, Aitken led Aberdeen to silverware when they won the Scottish League Cup on 26 November 1995, beating Dundee 2-0 in the final.

On 20 July 2006, he was named caretaker manager of Aston Villa after O'Leary's departure the previous evening.[10] Aitken managed Villa to three pre-season victories before being replaced by Martin O'Neill.[11]